NextGen Sequence Analysis

nextgen analysis Kenya

This hands-on training will equip participants with knowledge and skills on how to generate, manipulate, and analyze whole genome, whole exome, and targeted NGS data and discover germline SNPs, indels, SVs, and CNVs; somatic SNVs, SVs, and indels, and RNASeq SNPs and indels. The objective is to enhance the researchers‘ capacity to conduct world class scientific research and boost their institution‘s profile as a leading diagnostic and scientific centre.


The training is ideal for graduates in biological, medical, or agricultural sciences who are using or intend to use nextgen sequencing in their work. The training will teach you how to:

  • Learn the science, methods and applications of NGS.
  • Discover SNPs, SNVs, SVs, indels and CNVs from large genetic datasets
  • Identify varinats of clinical significance and diagnose medical conditions.
  • Optimize therapy and precision medicine

Continue Reading »


Dates: Every second and third weeks of the month
Duration: 10 days.
Venue: Nairobi, Kenya.

This practical training is ideal for graduates in biological, medical, or agricultural sciences who are using or intend to use nextgen sequencing in their work.

  • Kshs. 100,000/- (Inclusive of VAT 16%) for East African residents. Non-East African students pay 25% more on all charges.Fee covers tuition, training material, certificate, drinks and meals only.

  • Groups with a minimum of 5 people will enjoy a 10% discount and early bird registration (at least 2 weeks before the start) will be offered a 5% discount
  • Terms and conditions of Payments:

  • Fees are payable strictly in advance, (4 working days before the starting date). Cancellations made within 5 working days of a course will incur a 20% cancellation fee. We regret that no cancellations will be accepted within 2 working days of a course, but substitutions may be made.No
  • Fee is payable by bankers cheque or cash deposit to: Fee is payable by bankers cheque or MPESA to: Bioinformatics Institute of Kenya. A/C No. 01192845321700, Cooperative Bank, Co-op House Branch, Nairobi, Kenya. SWIFT Code KCOOKENAXXX. Branch Code: XXX. MPESA PAY BILL: Business number: 400222. Account number: 1679821#NGS. PAYPAL:


To register, please download the booking form fill it and send it to us through: Email:

SRA Tools, GATK, Picard, IGV, Bowtie-2, BBMap, FastQC, R, Biolinux, Oracle VirtualBox, Sam Tools, Velvet, IGV, NCBI Tools, HapMap, PLINK, SKAT-O, Broad Institute Resource Bundle, KENCLUST, 1,000 Genomes Project, The Cancer Genome Atlas (TCGA).
Course material including a comprehensive training manual and a CD with software

1. Installing and running Biolinux on Oracle Virtual Box

2. Biolinux commandline

3. Short read quality control

4. Introduction to the SRA

5. Understanding the fastq, SAM, and BAM formats

6. File conversion using Sam Tools and SRA tools

7. Reference mapping assembly using BBMap

8. Variant calling

9. De novo assembly using Velvet

10. Rna seq mapping and assembly

11. Phylogeny-based methods for analysis of genomes and metagenomes

12. Genome comparison and phylogeny

13. Exercises

14. Award of certificates